convert MZmine export csv file to biom file

[Lanying Ma]

Hi, 

I am new to use Qemistree and i successfully run through the tutorial of Qemistree with your demonstration files of feature table.  I want to create my own feature table now and i cant do it. 

the input file is the csv file from MZmine. 

i try to use it as 

biom convert -i moffitt_pos.csv -o feature-table.biom --process-obs-metadata sc_separated

I am actually not sure whether the above command is correct. Could you please help me out on this one?

Best

lan

[Lanying Ma]

I have coverted the .csv file to txt file, then from txt file to biom file. 

the command i used is: 

cut -d, -f3 test.csv | sed 's/"//g' > test.txt

biom convert -i test.txt -o feature-table.biom --to-hdf5

I got the pipeline to run until:

qiime qemistree make-hierarchy \

  --i-csi-results fingerprints.qza \

  --i-feature-tables feature-table.qza \

  --o-tree qemistree.qza \

  --o-feature-table feature-table-hashed.qza \

  --o-feature-data feature-data.qza

with error message as "Plugin error from qemistree:

  Cannot have empty feature table

Debug info has been saved to /tmp/qiime2-q2cli-err-26vob1vk.log". 

I checked the file size and found the input files are not empty.

 -rw-rw-r-- 1 ubuntu ubuntu    6990 Feb  1 23:39 feature-table.qza

-rw-rw-r-- 1 ubuntu ubuntu 1313590 Feb  1 23:58 fingerprints.qza

Do you have any idea of why i got the above error ? Thank you in advance.

Lan

[Louis-Félix Nothias]

Hi lan,

Are you able to run a test job with demo files ?

For support, I would suggest to open an issue on that repository:

https://github.com/biocore/q2-qemistree